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Metagenomics of Human Gut Microbiota
Overview of Human Gut Bacteria: The human gastrointestinal tract is home to an incredibly vast, highly-complex array of microbes. The number of bacteria present in the human gut is estimated to be greater than 200 billion, and the collective genome of these microbes is about 150 times the number of genes comprising the human genome. Thus, bacteria play a significant role in the lives of humans--much more so than is realized. The bacteria of the gut equip humans with a wide range of safeguards and benefits, from boosting immunity and decreasing the likelihood of serious diseases like cancer, to regulating metabolism, maintaining a healthy weight, and preventing bad breath and constipation. Without rich microbial flora, the human body would not function optimally, and could even risk fatality. Thus, the study of this diverse ecosystem is of great interest to scientists, medical researchers, and those generally concerned with their health and wellbeing. The Case for Metagenomic Study of Gut Microbes: While traditional methods like PCR and fluorescent in situ hybridization (FISH) have and continue to be used to study individual gut bacteria, only metagenomic analyses allow for a full-spectrum, all-inclusive assessment of the billions of organisms that inhabit this region. As stated in "Metagenomics: Key to Human Gut Microbiota," the scientific paper primarily analyzed in this Wikia, "Metagenomics refers to culture-independent and sequencing-based studies of the collective set of genomes of mixed microbial communities (metagenomes), aimed at exploring their compositional and functional characteristics." By analyzing gut microbes metagenomically, we are able to explore how a diverse group of species is able to function collectively to provide optimal conditions for the human host. Rather than assessing the presence and function of just acidophilus bacteria, for instance, metagenomic analyses allow us to see how acidophilus resides with, say, Helicobacter pylori, and how they are able to function in concert with one another. Procedure & Mechanism for a Metagenomic Study of Gut Bacteria: Metagenomic analysis of gut microbiota occurs when target regions of the 16S rRNA genes are amplified-- particularly regions V1, V2, V3, and V6 have been used for studying the human gastrointestinal ecosystem. Two main platforms have been developed for conducting metagenomic studies. The first is a Genome Sequencer 454 FLX system, which produces about 400,000 reads with average lengths of 250–350 base pairs (a read size sufficient to cover most of the variable regions in the 16S rRNA gene). The second is the Illumina Genome Analyzer system, which produces more than ten times the number of reads per run as the 454 FLX system, with average lengths of 35–75 base pairs. Through these metagenomic techniques, it has been discovered that, despite the enormous quantity of microbes in the human gut, there exists a surprising amount of homogeneity in the actual types of bacteria present in one individual. Of the 70 gut bacteria phyla known to date, metagenomic studies have determined that 90% of those in any one human's gut are made up of just 2 distinct phyla: Firmicutes (Gram-postive bacteria) and Bacteroidetes (Gram-negative bacteria). The remaining 10% is comprised of Acidobacteria, Actinobacteria, and various other microbes that can vary from individual to individual. Thus, metagenomic studies of gut bacteria have not only allowed us to identify the main types of microbes present in the GI tract, but also the fact that these bacteria can be highly individualized based on the host and the health of the host. Though a sizable number of gut bacteria are known, most humans possess just a couple types in large quantities. Gut Microbes and Health: While medical specialists have often focused on understanding the function of the human organs--the purpose of the gastrointestinal tract for excreting waste, et cetera--this is an incomplete mode. Studies on the microflora have allowed us to understand that, indeed, the bacteria of the gut are just as crucial to a properly-functioning digestive system as are the proper workings of the actual organs making up this system. Without a hearty population of gut microbes, we are not able to break down our food as efficiently, leading to the potential of malnutrition, irritable bowel syndrome, and other digestive maladies. Moreover, it has been shown that humans who have received both short and long courses of broad-spectrum antibiotics (Bactrim, Doxycycline), often experience upset stomach, increased susceptibility to illness, and even weight gain--the result of an upset in the microbiota of the gut. Thus, it is important to understand both the variety and function of the the bacteria present in our gasrointestinall tract in order to promote better health, and comprehensive metagenomic studies have allowed great advances in doing just this. References: Brandlow, HL. "Obesity and the Gut Microbiome." PubMed. 2014 Griffiths E, Gupta RS. (2001) "The Use of Signature Sequences and Bacterial Divisions. ''Microbiology''147:2611-22 Maccaferri, Simone et al. "Metagenomics: Key to Human Gut Microbiota." Department of Pharmaceutical Sciences, University of Bologna. 2011, Karger Ag, Basel (PubMed) Marchesi, JR. "Prokaryotic and Eukaryotic Diversity of the Human Gut." Advanced Applications of Microbiology 2010;72:43–62.